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Identification of genes responsible for human congenital disorders of these nerves, combined with the analysis of their role in axonal development in animal models, has advanced understanding of how neuromuscular connectivity is established. Here, we focus on the ocular motor system, as an instructive example of the success of this approach in unravelling the aetiology of human strabismus. The discovery that ocular motility disorders can arise from mutations in transcription factors, including <jats:italic>HoxA1<\/jats:italic>, <jats:italic>HoxB1<\/jats:italic>, <jats:italic>MafB<\/jats:italic>, <jats:italic>Phox2A<\/jats:italic>, and <jats:italic>Sall4<\/jats:italic>, has revealed gene regulatory networks that pattern the brainstem and\/or govern the differentiation of cranial motor neurons. Mutations in genes involved in axon growth and guidance disrupt specific stages of the extension and pathfinding of ocular motor nerves, and have been implicated in human strabismus. These genes encompass varied classes of molecule, from receptor complexes to dynamic effectors to cytoskeletal components, including <jats:italic>Robo3\/Rig1<\/jats:italic>, <jats:italic>Alpha2\u2010chimaerin<\/jats:italic>, <jats:italic>Kif21A<\/jats:italic>, <jats:italic>TUBB2<\/jats:italic>, and <jats:italic>TUBB3<\/jats:italic>. A current challenge is to understand the protein regulatory networks that link the cell surface to the cytoskeleton and to dissect the co\u2010ordinated signalling cascades and motile responses that underpin axonal navigation. Here we review recent insights derived from basic and clinical science approaches, to show how, by capitalising on the strengths of each, a more complete picture of the aetiology of human congenital cranial dysinnervation disorders can be achieved. This elucidation of these principles illustrates the success of clinical genetic studies working in tandem with molecular and cellular models to enhance our understanding of human disease. \u00a9 2016 Wiley Periodicals, Inc. 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